Methods for trait mapping in plants

Abstract

The present invention provides methods for identifying the nucleic acid sequences responsible for phenotypic traits in plants.

Description

CROSS REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority from U.S. Provisional Application Ser. No. 61 / 296,253 filed (Jan. 19, 2010) and U.S. Provisional Application Ser. No. 61 / 378,644 filed (Aug. 31, 2010), both of which are incorporated by reference herein in their entirety.FIELD OF INVENTION[0002]This invention is in the field of plant breeding. More specifically, this invention relates to the use of high throughput sequencing and marker discovery technologies for identifying polymorphisms and genes responsible for phenotypic traits in plants.BACKGROUND OF INVENTION[0003]The primary objectives of plant breeding are to select an optimal pair of parents to make a cross and then to select one or more superior progeny resulting from that cross. In hybrid crops, a third objective is to identify a tester to make up high performing hybrid seed. Traditional plant breeding has relied on visual observations and performance data on the plants or lines in order to make ...

AI Technical Summary

Benefits of technology

[0028]As used herein, a nucleic acid sequence can comprise 1 or more nucleotides (for example, 2 or more nucleotides, 25 or more nucleotides, 250 or more nucleotides, 1,000 or more nucleotides, even 20,000 or more nucleotides). In certain embodiments, adjacent nucleic acid sequence fragments can be ligated in vitro or aligned in silico for the purpose of obtaining a longer nucleic acid sequence. As used herein, a nucleic acid sequence from each of two or more individual plants from the same genomic region, that may or may not be associated with one or more phenotypic trait values, provides the basis for decisions related to germplasm improvement activities, wherein one or more loci can be evaluated. Knowing whether two sequences at a locus are completely identical or if they contain combinations of identical and non-identical loci can aid in determining whether the loci have the same trait value, are linked to the same traits or are identical by descent. Therefore in another aspect, one or more nucleic acid sequences from one or more individual plants that are associated with a phenotypic trait value can provide the basis for decisions related to germplasm improvement activities.

[0029]As used herein, the term “haplotype” means a chromosomal region within a haplotype window. Typically, the unique marker fingerprint combinations in each haplotype window define and differentiate individual haplotypes for that window. As used herein, a haplotype is defined and differentiated by one or more nucleic acid sequences at one or more loci within a “haplotype window.”

[0030]As used herein, the term “haplotype window” means a chromosomal region that is established by statistical analyses known to those of skill in the art and is in linkage disequilibrium. In the art, identity by state between two inbred individuals (or two gametes) at one or more molecular marker loci located within this region is taken as evidence of identity-by-descent of the entire region, wherein each haplotype window includes at least one polymorphic molecular marker. As used herein, haplotype windows are defined by two or more nucleic acid seque...

Problems solved by technology

However, SNP markers are still an indirect tool for querying underlying sequence and a SNP marker is restricted to only detecting two alleles, not the four possible nucleotides that might be found at any given nucleotide position.

However, these traditional marker discovery platforms are suboptimal because they are not suited for automati...